WormCG

I've found a number of data sources that contain cell lineage and position information for the C. elegans embryo but they are not in a common format, or they are embedded in a scholarly paper. I've started building a "data warehouse" to store all this data in a common format, called WormCG (for worm computational geometry). The design is very loosely based on BioWarehouse.

To start, WormCG will only contain cell position information. I plan to extend it to include the cell outline and other features, but I have yet to see a data source for that type of data (so I may be going through images and tracing the data).

Once I have some initial data imported, I'll begin writing some tools to pull it out and visualize it. I did a quick spike where I created a 3D volume in nrrd format and used 3DSlicer to examine it, and that seems like a good initial approach. 3DSlicer is a wonderful program, but it does not have any 4D support (or if it does, I haven't been able to find it).

The code for WormCG will be posted on the sourceforge site within a week or two.